JAL-1551 JAL-962 formatting and code change ripples from changing HiddenColumns ...

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 691aa17..f4cfc3f 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1685,11 +1685,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       copiedHiddenColumns = new Vector();
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
-      for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
-              .size(); i++)
+      for (int[] region : viewport.getColumnSelection().getHiddenColumns())
       {
-        int[] region = (int[]) viewport.getColumnSelection()
-                .getHiddenColumns().elementAt(i);
 
         copiedHiddenColumns.addElement(new int[]
         { region[0] - hiddenOffset, region[1] - hiddenOffset });

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 3e81664..776443f 100755 (executable)
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -713,11 +713,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
     if (av.hasHiddenColumns())
     {
       jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();
-      for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
+      for (int[] region : av.getColumnSelection().getHiddenColumns())
       {
-        int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
-                .elementAt(i);
-
         jalview.appletgui.AlignFrame.copiedHiddenColumns
                 .addElement(new int[]
                 { region[0], region[1] });

diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index 60d89aa..f888e3a 100755 (executable)
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -20,12 +20,23 @@
  */
 package jalview.appletgui;
 
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceGroup;
 import jalview.util.MessageManager;
 
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.PopupMenu;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+
 public class ScalePanel extends Panel implements MouseMotionListener,
         MouseListener
 {
@@ -97,7 +108,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
         });
         pop.add(item);
 
-        if (av.getColumnSelection().getHiddenColumns().size() > 1)
+        if (av.getColumnSelection().hasHiddenColumns())
         {
           item = new MenuItem(MessageManager.getString("action.reveal_all"));
           item.addActionListener(new ActionListener()
@@ -323,10 +334,8 @@ public class ScalePanel extends Panel implements MouseMotionListener,
     res = av.getColumnSelection().adjustForHiddenColumns(res);
 
     reveal = null;
-    for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
+    for (int[] region : av.getColumnSelection().getHiddenColumns())
     {
-      int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
-              .elementAt(i);
       if (res + 1 == region[0] || res - 1 == region[1])
       {
         reveal = region;
@@ -407,18 +416,18 @@ public class ScalePanel extends Panel implements MouseMotionListener,
         }
 
         gg.drawLine(
-                (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
                 y + 2,
-                (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
                 y + (fm.getDescent() * 2));
 
       }
       else
       {
         gg.drawLine(
-                (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
                 y + fm.getDescent(),
-                (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
                 y + (fm.getDescent() * 2));
       }
     }

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 53cca3c..81e5dae 100755 (executable)
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -20,9 +20,16 @@
  */
 package jalview.appletgui;
 
-import java.awt.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
 
 public class SeqCanvas extends Panel
 {
@@ -516,7 +523,8 @@ public class SeqCanvas extends Panel
     }
     else
     {
-      java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
+      java.util.List<int[]> regions = av.getColumnSelection()
+              .getHiddenColumns();
 
       int screenY = 0;
       int blockStart = startRes;
@@ -524,7 +532,7 @@ public class SeqCanvas extends Panel
 
       for (int i = 0; i < regions.size(); i++)
       {
-        int[] region = (int[]) regions.elementAt(i);
+        int[] region = regions.get(i);
         int hideStart = region[0];
         int hideEnd = region[1];
 
@@ -646,7 +654,7 @@ public class SeqCanvas extends Panel
 
     if ((group == null) && (av.getAlignment().getGroups().size() > 0))
     {
-      group = (SequenceGroup) av.getAlignment().getGroups().get(0);
+      group = av.getAlignment().getGroups().get(0);
       groupIndex = 0;
     }
 
@@ -803,7 +811,7 @@ public class SeqCanvas extends Panel
           break;
         }
 
-        group = (SequenceGroup) av.getAlignment().getGroups()
+        group = av.getAlignment().getGroups()
                 .get(groupIndex);
       } while (groupIndex < av.getAlignment().getGroups().size());
 

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index 529891f..a55f676 100644 (file)
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -20,7 +20,7 @@
  */
 package jalview.datamodel;
 
-import java.util.Vector;
+import java.util.List;
 
 public class CigarArray extends CigarBase
 {
@@ -148,25 +148,25 @@ public class CigarArray extends CigarBase
    * internal constructor function - called by CigarArray(AlignmentI, ...);
    * 
    * @param alignment
-   * @param columnSelection
+   * @param list
    *          - vector of visible regions as returned from
    *          columnSelection.getHiddenColumns()
    * @param selectionGroup
    */
   private void constructFromAlignment(AlignmentI alignment,
-          Vector columnSelection, SequenceGroup selectionGroup)
+          List<int[]> list, SequenceGroup selectionGroup)
   {
     int[] _startend = _calcStartEndBounds(alignment, selectionGroup);
     int start = _startend[1], end = _startend[2];
     // now construct the CigarArray operations
-    if (columnSelection != null)
+    if (list != null)
     {
       int[] region;
       int hideStart, hideEnd;
       int last = start;
-      for (int j = 0; last < end & j < columnSelection.size(); j++)
+      for (int j = 0; last < end & j < list.size(); j++)
       {
-        region = (int[]) columnSelection.elementAt(j);
+        region = list.get(j);
         hideStart = region[0];
         hideEnd = region[1];
         // edit hidden regions to selection range

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 97b7c67..f1c6cc4 100644 (file)
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -35,7 +35,7 @@ public class ColumnSelection
   Vector selected = new Vector();
 
   // Vector of int [] {startCol, endCol}
-  Vector hiddenColumns;
+  Vector<int[]> hiddenColumns;
 
   /**
    * Add a column to the selection
@@ -208,7 +208,7 @@ public class ColumnSelection
       int hSize = hiddenColumns.size();
       for (int i = 0; i < hSize; i++)
       {
-        int[] region = (int[]) hiddenColumns.elementAt(i);
+        int[] region = hiddenColumns.elementAt(i);
         if (region[0] > start && start + change > region[1])
         {
           deletedHiddenColumns.add(region);
@@ -263,7 +263,7 @@ public class ColumnSelection
     {
       for (int i = 0; i < hiddenColumns.size(); i++)
       {
-        int[] region = (int[]) hiddenColumns.elementAt(i);
+        int[] region = hiddenColumns.elementAt(i);
         if (region[0] >= start)
         {
           region[0] -= change;
@@ -484,7 +484,7 @@ public class ColumnSelection
    *          int
    * @return Vector
    */
-  public Vector getHiddenColumns()
+  public List<int[]> getHiddenColumns()
   {
     return hiddenColumns;
   }
@@ -503,7 +503,7 @@ public class ColumnSelection
     {
       for (int i = 0; i < hiddenColumns.size(); i++)
       {
-        int[] region = (int[]) hiddenColumns.elementAt(i);
+        int[] region = hiddenColumns.elementAt(i);
         if (result >= region[0])
         {
           result += region[1] - region[0] + 1;
@@ -531,7 +531,7 @@ public class ColumnSelection
       int[] region;
       do
       {
-        region = (int[]) hiddenColumns.elementAt(index++);
+        region = hiddenColumns.elementAt(index++);
         if (hiddenColumn > region[1])
         {
           result -= region[1] + 1 - region[0];
@@ -557,7 +557,7 @@ public class ColumnSelection
       int gaps = 0;
       do
       {
-        int[] region = (int[]) hiddenColumns.elementAt(index);
+        int[] region = hiddenColumns.elementAt(index);
         if (hiddenRegion == 0)
         {
           return region[0];
@@ -588,7 +588,7 @@ public class ColumnSelection
       int index = 0;
       do
       {
-        int[] region = (int[]) hiddenColumns.elementAt(index);
+        int[] region = hiddenColumns.elementAt(index);
         if (alPos < region[0])
         {
           return region[0];
@@ -616,7 +616,7 @@ public class ColumnSelection
       int index = hiddenColumns.size() - 1;
       do
       {
-        int[] region = (int[]) hiddenColumns.elementAt(index);
+        int[] region = hiddenColumns.elementAt(index);
         if (alPos > region[1])
         {
           return region[1];
@@ -652,7 +652,7 @@ public class ColumnSelection
 
     for (int i = 0; i < hiddenColumns.size(); i++)
     {
-      int[] region = (int[]) hiddenColumns.elementAt(i);
+      int[] region = hiddenColumns.elementAt(i);
       if (start <= region[1] && end >= region[0])
       {
         hiddenColumns.removeElementAt(i);
@@ -719,7 +719,7 @@ public class ColumnSelection
     {
       for (int i = 0; i < hiddenColumns.size(); i++)
       {
-        int[] region = (int[]) hiddenColumns.elementAt(i);
+        int[] region = hiddenColumns.elementAt(i);
         for (int j = region[0]; j < region[1] + 1; j++)
         {
           addElement(j);
@@ -734,7 +734,7 @@ public class ColumnSelection
   {
     for (int i = 0; i < hiddenColumns.size(); i++)
     {
-      int[] region = (int[]) hiddenColumns.elementAt(i);
+      int[] region = hiddenColumns.elementAt(i);
       if (res == region[0])
       {
         for (int j = region[0]; j < region[1] + 1; j++)
@@ -758,7 +758,7 @@ public class ColumnSelection
     {
       for (int i = 0; i < hiddenColumns.size(); i++)
       {
-        int[] region = (int[]) hiddenColumns.elementAt(i);
+        int[] region = hiddenColumns.elementAt(i);
         if (column >= region[0] && column <= region[1])
         {
           return false;
@@ -792,7 +792,7 @@ public class ColumnSelection
         for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++)
         {
           int[] rh, cp;
-          rh = (int[]) copy.hiddenColumns.elementAt(i);
+          rh = copy.hiddenColumns.elementAt(i);
           if (rh != null)
           {
             cp = new int[rh.length];
@@ -821,7 +821,7 @@ public class ColumnSelection
       for (i = 0; i < iSize; i++)
       {
         StringBuffer visibleSeq = new StringBuffer();
-        Vector regions = getHiddenColumns();
+        List<int[]> regions = getHiddenColumns();
 
         int blockStart = start, blockEnd = end;
         int[] region;
@@ -829,7 +829,7 @@ public class ColumnSelection
 
         for (int j = 0; j < regions.size(); j++)
         {
-          region = (int[]) regions.elementAt(j);
+          region = regions.get(j);
           hideStart = region[0];
           hideEnd = region[1];
 
@@ -886,7 +886,7 @@ public class ColumnSelection
     if (hiddenColumns != null && hiddenColumns.size() > 0)
     {
       Vector visiblecontigs = new Vector();
-      Vector regions = getHiddenColumns();
+      List<int[]> regions = getHiddenColumns();
 
       int vstart = start;
       int[] region;
@@ -894,7 +894,7 @@ public class ColumnSelection
 
       for (int j = 0; vstart < end && j < regions.size(); j++)
       {
-        region = (int[]) regions.elementAt(j);
+        region = regions.get(j);
         hideStart = region[0];
         hideEnd = region[1];
 
@@ -972,14 +972,14 @@ public class ColumnSelection
       // then mangle the alignmentAnnotation annotation array
       Vector annels = new Vector();
       Annotation[] els = null;
-      Vector regions = getHiddenColumns();
+      List<int[]> regions = getHiddenColumns();
       int blockStart = start, blockEnd = end;
       int[] region;
       int hideStart, hideEnd, w = 0;
 
       for (int j = 0; j < regions.size(); j++)
       {
-        region = (int[]) regions.elementAt(j);
+        region = regions.get(j);
         hideStart = region[0];
         hideEnd = region[1];
 

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b19e54f..235deda 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1767,20 +1767,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
 
-    Vector hiddenColumns = null;
+    ArrayList<int[]> hiddenColumns = null;
     if (viewport.hasHiddenColumns())
     {
-      hiddenColumns = new Vector();
+      hiddenColumns = new ArrayList<int[]>();
       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
               .getSelectionGroup().getEndRes();
-      for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
-              .size(); i++)
+      for (int[] region : viewport.getColumnSelection().getHiddenColumns())
       {
-        int[] region = (int[]) viewport.getColumnSelection()
-                .getHiddenColumns().elementAt(i);
         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
         {
-          hiddenColumns.addElement(new int[]
+          hiddenColumns.add(new int[]
           { region[0] - hiddenOffset, region[1] - hiddenOffset });
         }
       }
@@ -2107,10 +2104,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         if (Desktop.jalviewClipboard != null
                 && Desktop.jalviewClipboard[2] != null)
         {
-          Vector hc = (Vector) Desktop.jalviewClipboard[2];
-          for (int i = 0; i < hc.size(); i++)
+          List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
+          for (int[] region : hc)
           {
-            int[] region = (int[]) hc.elementAt(i);
             af.viewport.hideColumns(region[0], region[1]);
           }
         }
@@ -2167,10 +2163,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       if (Desktop.jalviewClipboard != null
               && Desktop.jalviewClipboard[2] != null)
       {
-        Vector hc = (Vector) Desktop.jalviewClipboard[2];
-        for (int i = 0; i < hc.size(); i++)
+        List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
+        for (int region[] : hc)
         {
-          int[] region = (int[]) hc.elementAt(i);
           af.viewport.hideColumns(region[0], region[1]);
         }
       }

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 97499c9..f732a36 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -47,8 +47,8 @@ import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.awt.geom.AffineTransform;
 import java.awt.image.BufferedImage;
+import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Vector;
 import java.util.regex.Pattern;
 
 import javax.swing.JCheckBoxMenuItem;
@@ -872,16 +872,13 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     Toolkit.getDefaultToolkit().getSystemClipboard()
             .setContents(new StringSelection(output), Desktop.instance);
 
-    Vector hiddenColumns = null;
+    ArrayList<int[]> hiddenColumns = null;
     if (av.hasHiddenColumns())
     {
-      hiddenColumns = new Vector();
-      for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
+      hiddenColumns = new ArrayList<int[]>();
+      for (int[] region : av.getColumnSelection().getHiddenColumns())
       {
-        int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
-                .elementAt(i);
-
-        hiddenColumns.addElement(new int[]
+        hiddenColumns.add(new int[]
         { region[0], region[1] });
       }
     }

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index c96b717..9bb27ed 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1257,8 +1257,8 @@ public class Jalview2XML
           for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
                   .size(); c++)
           {
-            int[] region = (int[]) av.getColumnSelection()
-                    .getHiddenColumns().elementAt(c);
+            int[] region = av.getColumnSelection()
+                    .getHiddenColumns().get(c);
             HiddenColumns hc = new HiddenColumns();
             hc.setStart(region[0]);
             hc.setEnd(region[1]);

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 01e4284..32773b9 100755 (executable)
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -128,7 +128,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
         });
         pop.add(item);
 
-        if (av.getColumnSelection().getHiddenColumns().size() > 1)
+        if (av.getColumnSelection().hasHiddenColumns())
         {
           item = new JMenuItem(
                   MessageManager.getString("action.reveal_all"));
@@ -371,24 +371,21 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
     reveal = null;
     if (av.getColumnSelection().getHiddenColumns() != null)
     {
-    for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
-    {
-      int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
-              .elementAt(i);
-      if (res + 1 == region[0] || res - 1 == region[1])
-      {
-        reveal = region;
-        ToolTipManager.sharedInstance().registerComponent(this);
-        this.setToolTipText(MessageManager
-                .getString("label.reveal_hidden_columns"));
-        break;
-      }
-      else
+      for (int[] region : av.getColumnSelection().getHiddenColumns())
       {
-        this.setToolTipText(null);
+        if (res + 1 == region[0] || res - 1 == region[1])
+        {
+          reveal = region;
+          ToolTipManager.sharedInstance().registerComponent(this);
+          this.setToolTipText(MessageManager
+                  .getString("label.reveal_hidden_columns"));
+          break;
+        }
+        else
+        {
+          this.setToolTipText(null);
+        }
       }
-
-    }
     }
     repaint();
   }

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 4d1546b..5032f69 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -34,6 +34,7 @@ import java.awt.Graphics2D;
 import java.awt.RenderingHints;
 import java.awt.Shape;
 import java.awt.image.BufferedImage;
+import java.util.List;
 
 import javax.swing.JComponent;
 
@@ -637,7 +638,7 @@ public class SeqCanvas extends JComponent
     }
     else
     {
-      java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
+      List<int[]> regions = av.getColumnSelection().getHiddenColumns();
 
       int screenY = 0;
       int blockStart = startRes;
@@ -645,7 +646,7 @@ public class SeqCanvas extends JComponent
 
       for (int i = 0; regions != null && i < regions.size(); i++)
       {
-        int[] region = (int[]) regions.elementAt(i);
+        int[] region = regions.get(i);
         int hideStart = region[0];
         int hideEnd = region[1];